I've run the same type of leagues, although much smaller (think single leagues) without minors, and OOTP creates players and FA at the right level. The PCMs are set such that any player created destined for a particular league will be created using that league's PCMs. So, if your leagues are all major league, then the PCMs will all be 1.000....
The one thing I'm not absolutely sure of is the amateur draft, as my leagues are before the amateur draft era, so I haven't enabled it yet. But a simple test will prove it out ... set up a your league, save it as world template, then sim it through the amateur draft. When the draft list is published, see what level those players are at. I think you'll be OK. Others may know better.
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